2024-01-21
This is PMA's DBGI daily open-notebook.
Today is 2024.01.21
Todo today
Have a look at the DBGI discussion forum
- https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Doing
Looking at https://www.youtube.com/watch?v=RE1hFm8lvJA&t=2s&ab_channel=InternationalSocietyforBiocuration
Ontology
An ontology is a formal specification of concepts, from a particular domain of knowledge, that are arranged in a hierarchy, as a directed acyclic graph, where concepts are defined in relation to other concepts in the graph.
KG
A knowledge graph (KG) is a graph that represents knowledge where entities are represented as nodes and relationships between these entities are represented as edges.
Graph formalisms:
- Property graphs
- RDF graphs
We allready had this discussion. Apparently Neo4j is a property graph. Which type of graph formalism are we looking for EMIKG ?
KGs are useful for graph-based machine learning
- Edge prediction
- Node classification
Biolink model
Created Biolink Model
Biolink model adopted in frame of the NCATS project.
- A high-level data model for representing biological and biomedical knowledge
- Bridges multiple vocabularies and ontologies
- Agnostic to the graph formalism used to represent knowledge
- The model consists of:
- Entities
- Associations
- Predicates
- Properties